GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Halopiger salifodinae KCY07-B2

Align Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate WP_049989937.1 LT39_RS07855 sugar ABC transporter permease

Query= TCDB::Q72H67
         (291 letters)



>NCBI__GCF_000784335.1:WP_049989937.1
          Length = 308

 Score =  178 bits (452), Expect = 1e-49
 Identities = 99/282 (35%), Positives = 158/282 (56%), Gaps = 8/282 (2%)

Query: 11  WILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQALW 70
           ++ ++P +++V +   YP+AQ  Y SFF   +   +  EFVGL NY  ++ +PD  Q LW
Sbjct: 25  YLPIVPVMVLVGVFILYPIAQAIYSSFFDKSLLSPDEAEFVGLANYQEIWTNPDLHQVLW 84

Query: 71  NTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQWMLNDV 130
           NT  +  V      V G  +  +++  F    +    +LIPW +P VV A +WQ+M    
Sbjct: 85  NTFVWVSVGSIAAIVFGFVLGWLLYEKFPYTSVASAIVLIPWVLPRVVGASIWQFMFGGD 144

Query: 131 YGVINVLGVKLGLLSQKVAFLARPEL-LLPSIIAVDVWKTTPFMALLLLAGLQMIPEELY 189
            G+IN L V+LG++ + +  L   +L L P II + +W+  P  ALL L  LQ I E LY
Sbjct: 145 QGIINELLVQLGVIDEYMVMLGSGDLSLWPPIIGM-IWRLAPLFALLTLTSLQGIDEHLY 203

Query: 190 EAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMS----GVNPATRT 245
           EAA +DGA+ W++F  ITLP++   L +  +   +  +R F +V+VM+    GV+ +T  
Sbjct: 204 EAARMDGATPWERFRYITLPMMRYNLAIGFLLMLIYNIRNFSMVWVMTEGGPGVSSSTLP 263

Query: 246 LAVYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTVGK 287
           + +Y R   VDF ++G  SA+SV + V++  F   Y++   K
Sbjct: 264 VMIY-RTAFVDF-NVGLASALSVLLFVVLLVFSYYYIKVYDK 303


Lambda     K      H
   0.329    0.142    0.433 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 252
Number of extensions: 9
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 291
Length of database: 308
Length adjustment: 27
Effective length of query: 264
Effective length of database: 281
Effective search space:    74184
Effective search space used:    74184
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory